Introduction
The RNA-seq*1 analysis pipeline has been provided by Rhelixa Corporation (CTO: Ryu Nakaki), which has a comprehensive collaboration agreement with the National Institute of Genetics, and implemented on the NIG supercomputer system.
*1: RNA-seq is a method for comprehensive analysis of gene expression using next generation sequencers. Unlike microarrays, which capture specific RNA sequences, RNA-seq can detect transcripts comprehensively. It is highly versatile as a method to obtain a large amount of RNA information, including unknown mRNA isoforms and splicing, by examining the sequence of the entire transcript. Therefor, it is used in a wide range of research fields to identify gene profiles in cells and narrow down genes with specific changes in expression.
What is the Rhelixa's RNA-seq analysis pipeline
This pipeline maps the Sequence Read Archive of a single sample obtained by the RNA-seq application to a reference genome, aggregates them by gene region and calculates the expression levels of all genes.
In this pipeline, the following processes can be executed collectively by simple command line operations.
- FastQC: Assess the quality of sequence reads contained in fastq files.
- Trimmomatic: Trim fastq files based on quality information.
- RSeQC: Get library strand information from fastq files.
- Hisat2: maps sequence reads in the fastq file to a reference genome*2.
- Samtools: Convert sam files obtained after mapping to bam files.
- featureCounts: Calculates the counts of the mapped reads for each gene.
*2: Only human (hg19, hg38) and mouse (mm9, mm10) reference genomes are supported.
How to use this analysis pipeline
Any user of the NIG supercomputer system can use this pipeline free of charge. If you require more advanced analysis, contact Rhelixa Co., Ltd.
About use
Contact Rhelixa
About Rhelixa Co., Ltd.
| Company Name | Rhelixa Co., Ltd. |
|---|---|
| Date of Establishment | February 2015 |
| Head Office | KDX Ginza East Building 5F, 3-7-2 Irifune, Chuo-ku, Tokyo |
| Representative | Ryu Nakaki |
| Main Business Activities | Consulting services for genomics and epigenetics research and business development using epigenomic data. |